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- PDB-2lg1: Solution structure of the human AKAP13 PH domain and stabilizing ... -

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Basic information

Entry
Database: PDB / ID: 2lg1
TitleSolution structure of the human AKAP13 PH domain and stabilizing DH helix
ComponentsA-kinase anchor protein 13
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


regulation of sarcomere organization / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / regulation of small GTPase mediated signal transduction / protein kinase A binding / positive regulation of Rho protein signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK ...regulation of sarcomere organization / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / MAP-kinase scaffold activity / cardiac muscle cell differentiation / regulation of Rho protein signal transduction / regulation of small GTPase mediated signal transduction / protein kinase A binding / positive regulation of Rho protein signal transduction / RHOB GTPase cycle / NRAGE signals death through JNK / adrenergic receptor signaling pathway / RHOC GTPase cycle / RHOA GTPase cycle / guanyl-nucleotide exchange factor activity / bone development / small GTPase binding / G alpha (12/13) signalling events / cell cortex / heart development / positive regulation of canonical NF-kappaB signal transduction / molecular adaptor activity / G protein-coupled receptor signaling pathway / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #2510 / RII binding domain / RII binding domain / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. ...Helix Hairpins - #2510 / RII binding domain / RII binding domain / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / C1-like domain superfamily / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Helix Hairpins / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
A-kinase anchor protein 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsLenoir, M. / Sugawara, M. / Ball, L. / Overduin, M.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Structural Insights into the Activation of the RhoA GTPase by the Lbc Oncoprotein.
Authors: Lenoir, M. / Sugawara, M. / Kaur, J. / Ball, L.J. / Overduin, M.
#1: Journal: Biomol.Nmr Assign. / Year: 2009
Title: Resonance assignments of the human AKAP13-PH domain and stabilizing DH helix.
Authors: Sugawara, M. / Whittaker, S.B. / Bishop, S. / Ball, L. / Overduin, M.
History
DepositionJul 19, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A-kinase anchor protein 13


Theoretical massNumber of molelcules
Total (without water)21,0551
Polymers21,0551
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein A-kinase anchor protein 13 / AKAP-13 / AKAP-Lbc / Breast cancer nuclear receptor-binding auxiliary protein / Guanine nucleotide ...AKAP-13 / AKAP-Lbc / Breast cancer nuclear receptor-binding auxiliary protein / Guanine nucleotide exchange factor Lbc / Human thyroid-anchoring protein 31 / Lymphoid blast crisis oncogene / LBC oncogene / Non-oncogenic Rho GTPase-specific GTP exchange factor / Protein kinase A-anchoring protein 13 / p47


Mass: 21055.184 Da / Num. of mol.: 1 / Fragment: PH domain residues 2164-2346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKAP13, BRX, HT31, LBC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Rosetta / References: UniProt: Q12802

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCO
1213D HN(CO)CA
131CBCA(CO)NH (H[N[co[{CA|ca[C]}]]])
1413D HN(CA)CB
1513D HNCA
161CCH TOCSY (hC CH.TOCSY)
1713D (H)CCH-TOCSY
1813D 1H-13C NOESY
1913D 1H-13C NOESY
11013D 1H-15N NOESY
11112D 1H-15N HSQC/HMQC

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Sample preparation

DetailsContents: 0.5 mM [U-100% 13C; U-100% 15N] AKAP13a_A10, 50.0 mM sodium phosphate, 150.0 mM sodium chloride, 0.1 mM Sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMAKAP13a_A10-1[U-100% 13C; U-100% 15N]1
50.0 mMsodium phosphate-21
150.0 mMsodium chloride-31
0.1 mMSodium azide-41
Sample conditionsIonic strength: 150.00 / pH: 7.00 / Pressure: 1.00 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian UnityInova / Manufacturer: Varian / Model: UnityInova / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.1Linge, O'Donoghue and Nilgesstructure
CcpNmr Analysis2.1CCPNassignment
NMRPipeNMRpipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ARIA2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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